Calcium in PDB 6bs2: Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B, PDB code: 6bs2 was solved by G.Kumar, Y.Wang, W.Li, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.101, 157.602, 181.509, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 23.4

The structure of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B (pdb code 6bs2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B, PDB code: 6bs2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:59.2 occ:1.00 OD1 A:ASP39 2.3 53.4 1.0 O A:THR41 2.4 66.7 1.0 OE1 A:GLU55 2.5 65.5 1.0 OD2 A:ASP39 2.5 54.8 1.0 O A:GLY44 2.6 56.9 1.0 OE2 A:GLU55 2.6 52.1 1.0 CG A:ASP39 2.8 53.5 1.0 OG1 A:THR41 2.9 63.5 1.0 CD A:GLU55 2.9 60.3 1.0 C A:THR41 3.5 64.3 1.0 C A:GLY44 3.5 61.0 1.0 CB A:THR41 3.6 63.2 1.0 CA A:THR41 4.0 64.5 1.0 N A:GLY45 4.2 60.5 1.0 CA A:GLY45 4.2 61.2 1.0 N A:THR41 4.3 61.7 1.0 CB A:ASP39 4.3 55.4 1.0 OD1 A:ASP47 4.4 54.9 1.0 CG A:GLU55 4.4 60.2 1.0 CZ A:PHE49 4.4 47.4 1.0 OD1 A:ASN50 4.5 49.2 1.0 CA A:GLY44 4.5 62.9 1.0 N A:GLY44 4.5 65.8 1.0 CE1 A:PHE49 4.6 48.0 1.0 CE1 A:HIS61 4.6 60.7 1.0 N A:ILE42 4.7 65.1 1.0 ND2 A:ASN50 4.7 45.2 1.0

Calcium binding site 2 out of 2 in the Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-RB3_SLD-Ttl in Complex with Heterocyclic Pyrimidine Compound 8B within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:37.7 occ:1.00 O C:THR41 2.3 43.3 1.0 OE1 C:GLU55 2.4 35.3 1.0 O C:GLY44 2.5 48.0 1.0 O C:HOH613 2.5 22.9 1.0 OD2 C:ASP39 2.5 44.5 1.0 OD1 C:ASP39 2.5 44.9 1.0 OE2 C:GLU55 2.5 42.4 1.0 OG1 C:THR41 2.6 37.7 1.0 CD C:GLU55 2.8 39.6 1.0 CG C:ASP39 2.9 44.2 1.0 C C:THR41 3.4 41.4 1.0 C C:GLY44 3.5 48.5 1.0 CB C:THR41 3.5 39.1 1.0 CA C:THR41 3.8 41.1 1.0 N C:THR41 4.1 39.1 1.0 CA C:GLY45 4.2 42.6 1.0 N C:GLY45 4.2 45.8 1.0 CG C:GLU55 4.3 34.2 1.0 CB C:ASP39 4.4 44.3 1.0 OD1 C:ASN50 4.4 35.5 1.0 CA C:GLY44 4.5 49.2 1.0 OD2 C:ASP47 4.5 43.3 1.0 N C:GLY44 4.5 49.1 1.0 N C:ILE42 4.5 40.5 1.0 CZ C:PHE49 4.6 34.7 1.0 NE2 C:HIS61 4.7 31.3 1.0 CE1 C:PHE49 4.8 27.9 1.0 ND2 C:ASN50 4.9 31.8 1.0 CG2 C:THR41 4.9 37.2 1.0 CA C:ILE42 5.0 42.6 1.0

S.Banerjee, K.E.Arnst, Y.Wang, G.Kumar, S.Deng, L.Yang, G.B.Li, J.Yang, S.W.White, W.Li, D.D.Miller. Heterocyclic-Fused Pyrimidines As Novel Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site: Structural Basis and Antitumor Efficacy. J. Med. Chem. V. 61 1704 2018.
ISSN: ISSN 1520-4804
PubMed: 29406710
DOI: 10.1021/ACS.JMEDCHEM.7B01858